Antibiotics and bacterial dysbiosis

I have all the symptoms of bacterial dysbiosis (bloating, pain, fatigue, brain fog, etc) and probably SIBO. I've tried every kind of probiotic you can imagine and I actually either feel worse after taking it or not affected at all. I've read that if you have SIBO, taking probiotics can make things worse since you already have too much bacteria growing in your upper gut and adding more in concentrated doses won't help until you've reduced the overgrowth already present. Some health practitioners recommend taking a course of antibiotics for this followed by probiotics to repopulate the gut, so I was thinking of doing that. However, I've also read some recent research suggesting that after antibiotics our good bacteria don't come back for a long time, and sometimes never come back http://www.wired.com/wiredscience/2011/08/killing-beneficial-bacteria/. I was wondering what everyone's thoughts on this are, and if I take antibiotics, how long should I take it for?

AHAH! My symptoms aren't extreme but it seems like my digestion has been very off ever since my appendectomy. I always thought it was because of scar tissue in my colon since my worst symptom has been chronic constipation. However, eating probiotic sauerkraut, yogurt, etc... + occasional rounds of probiotic supplements seems to help - only just so. What do you do about not having this colonic flora reservoir?

College -I tried GAPS for about 5months, same for SCD.
Update: Still trying the Ray peat thing -recently had Danny Roddy consult -he helped me tweak the diet and fix some major things I was missing/doing wrong. Just getting started on those adjustments.

I know I'm very late on this question, but Senneth - how long were you on GAPS? I had the same issues (albeit no SIBO - confirmed via test) and I have flourished on the SCD diet. I would encourage Chris to try it. Also, any updates since this post?

Yea that explains a lot. Being vegetarian alone could have caused the hypothyroidism since you probably weren't getting the raw materials your body needed for the production and signaling of thyroid hormone. If you go to levaquin's own page the first thing it says is "LEVAQUIN ® can cause side effects that may be serious or even cause death." That could definitely explain your dysbiosis as well. For me, I can't really pinpoint a time when my symptoms got really bad, it was a gradual progression, and I don't even know the extent of it since I can't afford testing.

Haha! I guess I should have mentioned my turning point -My tummy troubles all started with a heavy dose of Levaquin. I had the flu of some kind really really bad, so that is what the "doc" prescribed. (Pre-paleo/nutrition junkie days). It is known to cause liver damage, and that is what I got from it too! I did have a lot of low thyroid symptoms before that though, cold all the time, etc. Could be cause I was vegetarian for 5 years too. I am learning my lessons the hard way!

Having looked at these comments and done a quick search on glutamine, I am not going to give it another try. This doesn't always work for me, but yesterday I had three bottles of Yakult and after a couple of hours the sore tongue started improving. I don't think I have ever had any good results from dried probiotics (even the refrigerated ones).

Did about half hour of leg work for you and came up with Glenn Rexroad, Akron 330-929-2819. Seems real solid in ability (Over the phone?) $75 for 75 minutes. That's a good price! It will blow your mind how quickly you will feel results. I had a bout of dysbiosis that just ended after two sessions. good luck

Yea I read Jaminet's article where he says it can feed bad bacteria, yet so many natural health practitioners recommend it for leaky gut since it's used as a fuel to repair the gut lining. So there's conflicting evidence on it and I'm not sure which side is right. I do know that I can't handle too much due to the stimulatory effect it has on my brain.

Senneth, it's good you've pretty much ruled out most of the common causes of the symptoms you have. My guess is you started out with something that initially damaged your gut and continued to damage it over time, which caused dysbiosis, and that led to adrenal fatigue and hypothyroidism, I think that's the case with me too. I'm currently researching the link between dysbiosis and hypothyroidism and finding articles such as this http://drhedberg.com/2011/02/15/the-gut-thyroid-connection/ showing that dysbiosis in the gut can lead to hormonal imbalances.

Thanks for your advice Lucas, bacterial biofilms are something I definitely need to research. I think this is a subject that has vast unknowns and will be a key target for treating digestive problems in the future.

You may be interested in this http://www.aaqm.org/Downloads/aaqmdocMay08.pdf. I haven't done more research to verify the claim, but he claims enzymes can hurt you instead of help you if you have bacteria that have formed biofilms in your gut.

lol I believe you Senneth, you seem to have tried everything. I've read about certain enzymes that disrupt bacterial biofilms but I've never tried any, so I'm thinking of trying them. Sometimes when you try everything to heal the gut and kill bacteria and it doesn't work it could be candida overgrowth or a parasite, have you been tested for either of these?

I meant it when I said I have tried almost everything. My education is in research + I have a lot of free time + my goal in life is to feel better = tried a ton of stuff!!!
In fact the list that Lucas has given you was suggested to me by 2 different highly educated and experienced providers. It just didn't work for me.

Chris- I hate to shoot everything down, and something that didn't work for me, might work for you. I have tried 3 bottles of that biofilm distruptor by Klaire labs. Once when doing the rifaximin, once with another antibiotic, and once with an oil of oregano/collodial silver protocol. Just made my stomach hurt really really bad. No change to my symptoms.

Although I have been on that regime for 2 months plus a ton of dietary changes (100g a protein a day, plus many other things), you have to gradually step up the thyroid to get to the right dose. I have only been on the right dose for a couple of weeks. I am hoping that will get rid of the SIBO. I am 3.5 years in, so I don't expect a miracle. Slow improvement would be more realistic.

Chris -I do have adrenal fatigue (I took a month long saliva test). I am not currently focusing on treating that directly. I am hoping that treating the low thyroid and the dietary changes I made will help with that. I have read (I think on Lita Lee's site) that taking Adrenals/DHEA when your not in balance..can lead to those compounds being used by the body to create estrogen, which can further harm the thyroid/adrenals. (Don't quote me on that, I am still learning!). Working with Lita Lee (a Ray Peat prodigy), I am taking bovine whole thyroid, progesterone, pregnenalone, and a ton of enzymes

However, I think differences in levels of each bacteria will occur based on the individual, so maybe in that sense you could have different "kinds" of dysbiosis since there are so many different strains of bacteria that could overgrow relative to the others. I think the sum of evidence shows that it's excess carbs, especially bad carbs, that cause overgrowth of bad bacteria, not protein and fat. It's not the animal protein and fat in industrialized societies that is causing dysbiosis and gut damage, it's the trans and omega 6 fats and large amounts of sugar.

I would say that putrefaction dysbiosis is secondary to fermentation dysbiosis. In other words, you only start to have problems with digesting proteins and fat when you develop dysbiosis and leaky gut from a diet too high in things that damage the gut and cause the bad bacteria to grow such as sugar and grains. Really you could combine all these and say there is only one "kind" of dysbiosis cause if you have a deficiency of good bacteria you'll simultaneously have fermentation and possibly putrefaction.

Sensitization dysbiosis occurs when microbes in the gut produce toxins that the body recognizes as foreign. The body then activates an immune response to kill them. However, this response may result in autoimmune diseases such as rheumatoid arthritis, ankylosing spondylitis (impaired mobility of the spinal column), and eczema. Those with sensitization dysbiosis may experience food intolerances and leaky gut syndrome. As in fermentation dysbiosis, restrict carbohydrate consumption and use friendly bacteria. So there, hope I helped somehow and good luck. :)

Deficiency dysbiosis..this type of dysbiosis is a deficiency in good bacteria such as lactobacilli. Generally, the use of antibiotics and a low fiber intake is responsible for this. Deficiency dysbiosis is often seen in those with irritable bowel syndrome and food sensitivities. As this type of dysbiosis is often seen together with putrefaction dysbiosis, take the same steps.

Fermantation dysbiosis..foods are “fermented”within our bodies, resulting in bloating, constipation, diarrhea, fatigue, and gas. This generally occurs due to the maldigestion of carbohydrates such as sugars, fruit, beer, wine, grains, and fiber. To help eliminate fermentation dysbiosis, you must avoid carbohydrate-containing foods. A diet free of cereal grains and added sugars is helpful, and some people may have to avoid fruit, fat, and added sugars is helpful, and some people may have to avoid fruit, fat, and starchy vegetables.

i see..well i guess you should just look at the symptoms here and then determine what diet you should take.
Putrefaction dysbiosis occurs when we don't digest our food well, resulting in them rotting inside us. It is the most common type and may bring on bloating, discomfort, or indigestion. A diet high in animal fat and low in fiber is why this type of dysbiosis is so prevalent in many “industrialized” societies. So you may want to skip food that is very high in fat.

I agree that antibiotics often create more damage than they heal. I think doctors might be afraid that the more antibiotics they prescribe, especially when they're unnecessary, the more they're increasing resistant strains of bacteria. I'll try to increase the fiber in my diet, especially prebiotics as others have mentioned. I haven't been tested so I don't know the exact details of which bacteria are too high or low in my gut, it would def help me have a clearer picture of what's going on though.

Thanks for sharing your experience, don't pay attention to anyone who downvoted you. I haven't heard about molybdenum for brain fog, I'll have to research that. I've had the same excitatory effects with glutamine, I dunno why but it just stimulates me too much.

Thanks for the link, and you make a good point, I didn't know that about the oxalobacter bacteria. I'm definitely rethinking taking antibiotics. It seems as if certain species of bacteria require a very specific environment in which to grow and if that environment is drastically altered they simply can't repopulate the gut. Needless to say, there's still so much we don't know about the microbiome and whether or not this really is the case.

Thanks for your recommendations, I appreciate it. I'm gonna try to up my vit D intake and see if that helps. I've taken probiotics for many weeks and haven't seen improvement, so I've stopped them until I try another approach to dealing with my symptoms. I think you're right about not taking antibiotics except in the cases you mention.

Have you thought about reducing inflammation in the brain and healing the blood brain barrier? Chris Kresser says that many people who don't improve from focusing on the gut have a messed up gut-brain axis and need to focus on restoring brain function. This is something I've thought about a lot. The rationale is inflammation from the gut goes to the brain, makes the blood brain barrier more porous or "leaky" and disrupts the functioning of the vagus nerve, shutting down digestion and allowing bad bacteria to overgrow regardless of taking probiotics.

Thanks for sharing your experience Senneth, I can def relate to all the problems you've had. I suspect I have adrenal fatigue along with hypothyroidism, I have most if not all of the symptoms that go along with those conditions. I recently found out about this product called Paraplex http://healthy-information.naturalhealthdoc.net/STANDARD-PROCESS-INFORMATION-SHEET/Paraplex-Information.htm. It has thyroid hormone plus all the other important hormones combined in one product. I'm thinking of buying it. What product did you take for thyroid hormone, and what dose did you take?

Dean,
I disagree. Peat recommends carrots because they are so anti-bacterial and anti-fungal that they resist digestion from the bad bacteria, and are supposed to help kill them off. Also the carrots stimulate peristalsis which can help move bad bacteria down the line, and out of the body. Peat also suggest cooked bamboo shoots for the same effect. Other raw vegetables are the ones that are problematic, that is why Peat specifically recommends carrots.

You need to understand that Ray Peat recommends carrots to "soak up" toxins in the colon, but that's a problematic assumption. Reaching the colon partly undigested means the chyme can ferment. Raw vegetables are very hard to digest and should be avoided when someone has SIBO. Carrots are loaded with fructose and even gram amounts can be problematic in these cases.

"How did it make it worse?" - worsening of symptoms I had whenever I ate carbs/vegetables/FODMAPs
"What did the rest of your diet look like? Did you eat the carrot salad solo?" - I was VLC, raw carrots clearly stood out from the rest of my diet.
"Have you cured your digestive issue?" - short answer is yes. VLC works, but it takes time.

comment continued . . . the point of the above comment was to say, yes you are right; there are some bacteria that don't recolonize or recolonize reluctantly, especially in adults. I personally only will take an antibiotic as a last resort.

Found the link . . . I have severe oxalate issues, which may be in part because I killed off Oxalobacter formigenes by taking a lot of antibiotics (it's a bacteria that breaks down oxalate in the gut). According to the oxalate scientists at lowoxalate.info this bacteria often does not recolonize adults if it is depleted by antibiotic treatment. It only colonizes easily and reliably in infants/young children. So, if there's one bacteria that rarely recolonizes in adults, there must be others.

Found the link . . . I have severe oxalate issues, which may be in part because I killed off Oxalobacter formigenes by taking a lot of antibiotics (it's a bacteria that breaks down oxalate in the gut). According to the oxalate scientists at http://www.lowoxalate.info/ this bacteria often does not recolonize adults if it is depleted by antibiotic treatment. It only colonizes easily and reliably in infants/young children. So, if there's one bacteria that rarely recolonizes in adults, there must be others.

I have shared my own experience here in the hope that it might be of use to Chris and prompt others to share solutions to this problem. What is there in this answer that would prompt 2 x downvotes? I don't understand.

I haven't really tried the daily carrot salad full on as I don't have severe digestive issues but I've heard anecdotes that it can do wonders. This is in the context of a low fiber high sugar diet though. Carrots are cheap though and readily available so its worth a shot imo.

For all things regarding gut dysbiosis, Dr Art Ayers is the man. http://coolinginflammation.blogspot.com/ On the right side of the postings, he has the content of his postings by subject. He has a wealth of information.

I'm sure it's dysbiosis, I've researched it for years and fit all the symptoms to a T, but I def think other things are involved, adrenal fatigue being one. Thanks for the link though I'll take the quiz, I suspect I have many of the symptoms on it.

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I have been diagnosed with SIBO via a breath test, and matching symptoms to yours. I have battling it for over 3 years. I have tried EVERYTHING, so I might be kind of helpful to you, at least in ruling out things to try.

-Probiotics are hell for me and a huge waste of money!!!

-The Mark Pimentel protocols referenced by another answer was USELESS. I have taken two rounds of rifaximin at his suggested dose. (Plus another round of a different antibiotic). There was zero effect, including while I was on it -some people experience relief while on the antibiotic but not after). Mine was neither. Also I read somewhere that he has his hand in the honeypot for that drug. (Here is the article).

-Regarding Cliff's answer about the Peat carrot salad. I have been doing eating it daily, along with the pro-thyroid Peat diet for over 4 months with No effect.

I have literally tried everything from GAPS, to autohemotherapy, cleanses, chinese medicine ,eliminated everyfood (drank coffee and ate ice for weeks at one point in desperation to take a break from my damn digestion issues), consumed digestive enzymes to the tune of $200 a month worth, coconut oil every day for years....

What I am doing now is still the Ray Peat thing...however I am looking at SIBO strictly from a thyroid spin. Peat says that having chronically low thyroid allows bad bacteria to slowly creep up the digestive system, and a sure sign is small intestinal bacterial overgrowth. He also says that someone can have low thyroid but test normal, because of the expansive normal standards skewed by generations of low thyroid people. Going by the symptoms of low thyroid (including body temp and pulse rate), I have been experiencing low thyroid for years if not decades. It has taken a few months to get to the right dose of thyroid, and I have only been on the right dose for 2 weeks. But I feel like a different person -full of energy, warm, positive mood :except for my damn digestion!

So now, I am pinning all my hope that having a super great thyroid (and supporting it and my liver with the Peat diet suggestions), will allow my body to naturally get rid of the SIBO. I will keep you updated, and good luck!!

Although I have been on that regime for 2 months plus a ton of dietary changes (100g a protein a day, plus many other things), you have to gradually step up the thyroid to get to the right dose. I have only been on the right dose for a couple of weeks. I am hoping that will get rid of the SIBO. I am 3.5 years in, so I don't expect a miracle. Slow improvement would be more realistic.

Chris -I do have adrenal fatigue (I took a month long saliva test). I am not currently focusing on treating that directly. I am hoping that treating the low thyroid and the dietary changes I made will help with that. I have read (I think on Lita Lee's site) that taking Adrenals/DHEA when your not in balance..can lead to those compounds being used by the body to create estrogen, which can further harm the thyroid/adrenals. (Don't quote me on that, I am still learning!). Working with Lita Lee (a Ray Peat prodigy), I am taking bovine whole thyroid, progesterone, pregnenalone, and a ton of enzymes

Have you thought about reducing inflammation in the brain and healing the blood brain barrier? Chris Kresser says that many people who don't improve from focusing on the gut have a messed up gut-brain axis and need to focus on restoring brain function. This is something I've thought about a lot. The rationale is inflammation from the gut goes to the brain, makes the blood brain barrier more porous or "leaky" and disrupts the functioning of the vagus nerve, shutting down digestion and allowing bad bacteria to overgrow regardless of taking probiotics.

Thanks for sharing your experience Senneth, I can def relate to all the problems you've had. I suspect I have adrenal fatigue along with hypothyroidism, I have most if not all of the symptoms that go along with those conditions. I recently found out about this product called Paraplex http://healthy-information.naturalhealthdoc.net/STANDARD-PROCESS-INFORMATION-SHEET/Paraplex-Information.htm. It has thyroid hormone plus all the other important hormones combined in one product. I'm thinking of buying it. What product did you take for thyroid hormone, and what dose did you take?

I know I'm very late on this question, but Senneth - how long were you on GAPS? I had the same issues (albeit no SIBO - confirmed via test) and I have flourished on the SCD diet. I would encourage Chris to try it. Also, any updates since this post?

College -I tried GAPS for about 5months, same for SCD.
Update: Still trying the Ray peat thing -recently had Danny Roddy consult -he helped me tweak the diet and fix some major things I was missing/doing wrong. Just getting started on those adjustments.

For me, reducing carbs to less than 25g/day had a good effect on dysbiosis at first, in that the symptoms entirely went away. Unfortunately, I had to up the carbs (to address cortisol from the stress response resulting from low carb). A few weeks later, the dysbiosis started up quite badly. Just before the dysbiosis blew up, I increased magnesium supplementation a lot. I suspect this made the gut environment more alkaline and encouraged the overgrowth. I also suspect I started to get too liberal with the potatoes in the evening. I have cut back on the carbs and magnesium and I am seeing some improvement.

What helps me with some of the symptoms, brain fog, particularly, is molybdenum, which is a co-factor with the enzyme that deals with aldehydes. Glutathione is supposed to be good for aldehydes and brain fog but I am not sure it makes a difference. I remember once trying glutamine and it seemed to help a lot with brain fog and sore tongue. I was nervous about continuing it because of the excitatory effects, but I'm thinking of trying it again.

It will be good to hear how you get on - please keep posting on progress.

Found the link . . . I have severe oxalate issues, which may be in part because I killed off Oxalobacter formigenes by taking a lot of antibiotics (it's a bacteria that breaks down oxalate in the gut). According to the oxalate scientists at http://www.lowoxalate.info/ this bacteria often does not recolonize adults if it is depleted by antibiotic treatment. It only colonizes easily and reliably in infants/young children. So, if there's one bacteria that rarely recolonizes in adults, there must be others.

I have shared my own experience here in the hope that it might be of use to Chris and prompt others to share solutions to this problem. What is there in this answer that would prompt 2 x downvotes? I don't understand.

Thanks for sharing your experience, don't pay attention to anyone who downvoted you. I haven't heard about molybdenum for brain fog, I'll have to research that. I've had the same excitatory effects with glutamine, I dunno why but it just stimulates me too much.

Having looked at these comments and done a quick search on glutamine, I am not going to give it another try. This doesn't always work for me, but yesterday I had three bottles of Yakult and after a couple of hours the sore tongue started improving. I don't think I have ever had any good results from dried probiotics (even the refrigerated ones).

Yea I read Jaminet's article where he says it can feed bad bacteria, yet so many natural health practitioners recommend it for leaky gut since it's used as a fuel to repair the gut lining. So there's conflicting evidence on it and I'm not sure which side is right. I do know that I can't handle too much due to the stimulatory effect it has on my brain.

The human digestive track is a carnivorous one and doesn't rely on bacteria outside the colon. People can live without a colon, so that should tell you something. The appendix serves as a reservoir of colonic flora.

My experience with probiotics matches yours.

An alternative to antibiotics is a diet that will starve the bacteria. That means VLC/low residue or zero carb, unless you're ok with having to drink glucose filled liquids for weeks.

Walter Voegtlin talks about a similar diet - one that is optimal for human digestion and eradicating fermentative gut flora - in "The Stone Age Diet", which is available here.

The "Cedars Sinai" SIBO protocol by Mark Pimentel uses rifaximin for about a week... look into his book "A New IBS Solution".

AHAH! My symptoms aren't extreme but it seems like my digestion has been very off ever since my appendectomy. I always thought it was because of scar tissue in my colon since my worst symptom has been chronic constipation. However, eating probiotic sauerkraut, yogurt, etc... + occasional rounds of probiotic supplements seems to help - only just so. What do you do about not having this colonic flora reservoir?

This is highly empirical and theory-based. I would suggest the following (consult with your doctor first!):

Broad-spectrum antibiotics. This should help "resetting" the gut microbiota and reduce potential colonization resistance.

Concomitant supplementation with probiotics (Bifidobacteria and Lactobacillus). There are differences between strains, but most available probiotics use the strains known to compete with enteropathogens. Aside from direct competition, some produce anti-microbial molecules.

Supplementing with potential biofilm disruptors. There is an interesting laboratory which uses several enzymes shown to disrupt bacterial biofilms (1). However, I haven't seen hard evidence yet. Some natural plants can inhibit quorum sensing, like oregano, basil, rosemary, turmeric, berries, among other.

I meant it when I said I have tried almost everything. My education is in research + I have a lot of free time + my goal in life is to feel better = tried a ton of stuff!!!
In fact the list that Lucas has given you was suggested to me by 2 different highly educated and experienced providers. It just didn't work for me.

You may be interested in this http://www.aaqm.org/Downloads/aaqmdocMay08.pdf. I haven't done more research to verify the claim, but he claims enzymes can hurt you instead of help you if you have bacteria that have formed biofilms in your gut.

Senneth, it's good you've pretty much ruled out most of the common causes of the symptoms you have. My guess is you started out with something that initially damaged your gut and continued to damage it over time, which caused dysbiosis, and that led to adrenal fatigue and hypothyroidism, I think that's the case with me too. I'm currently researching the link between dysbiosis and hypothyroidism and finding articles such as this http://drhedberg.com/2011/02/15/the-gut-thyroid-connection/ showing that dysbiosis in the gut can lead to hormonal imbalances.

Chris- I hate to shoot everything down, and something that didn't work for me, might work for you. I have tried 3 bottles of that biofilm distruptor by Klaire labs. Once when doing the rifaximin, once with another antibiotic, and once with an oil of oregano/collodial silver protocol. Just made my stomach hurt really really bad. No change to my symptoms.

lol I believe you Senneth, you seem to have tried everything. I've read about certain enzymes that disrupt bacterial biofilms but I've never tried any, so I'm thinking of trying them. Sometimes when you try everything to heal the gut and kill bacteria and it doesn't work it could be candida overgrowth or a parasite, have you been tested for either of these?

Thanks for your advice Lucas, bacterial biofilms are something I definitely need to research. I think this is a subject that has vast unknowns and will be a key target for treating digestive problems in the future.

Haha! I guess I should have mentioned my turning point -My tummy troubles all started with a heavy dose of Levaquin. I had the flu of some kind really really bad, so that is what the "doc" prescribed. (Pre-paleo/nutrition junkie days). It is known to cause liver damage, and that is what I got from it too! I did have a lot of low thyroid symptoms before that though, cold all the time, etc. Could be cause I was vegetarian for 5 years too. I am learning my lessons the hard way!

Yea that explains a lot. Being vegetarian alone could have caused the hypothyroidism since you probably weren't getting the raw materials your body needed for the production and signaling of thyroid hormone. If you go to levaquin's own page the first thing it says is "LEVAQUIN ® can cause side effects that may be serious or even cause death." That could definitely explain your dysbiosis as well. For me, I can't really pinpoint a time when my symptoms got really bad, it was a gradual progression, and I don't even know the extent of it since I can't afford testing.

I'm not a doctor, and this is not medical advice, but this is how I got rid of my SIBO/IBS-D problem.

Avoid antibiotics UNLESS you have mutated microbes that can't be dealt with diet (e.g. protozoal, CDiff, H.Pylori, gardia parasites). You need to test for these specifically. Only get antibiotics if you have something like that. Most "normal" bacteria and yeast overgrowth can be dealt on with diet.

So, follow a strict Paleo diet (including offal, bone broths, coconut oil), and if you do dairy, only do goat dairy, and only lactose-free (home-made probiotic yoghurt, hard cheeses). Then, eat probiotic foods: sauerkraut, the goat yoghurt mentioned above, raw & unfiltered local honey, Yogi kombucha green tea decaf, and eat some prEbiotic foods too (list of prebiotic foods on wikipedia). Last but not least, supplement with D3+K2+Mg (and Ca if you don't do dairy), and alternate it daily with krill oil and a multi-vitamin (Nature's Way Alive is the one I use). Get a multi-probiotic pill (I prefer iFlora) just before you go to bed. Probiotics will make you feel worse for a week, but then your body learns to deal with them.

With this regime, I went from 4-5 diarrhea episodes a day, to having one solid, healthy stool every day, within 20-45 minutes of waking up. I saw changes within the first few days, but it took about a month to get there overall.

Thanks for your recommendations, I appreciate it. I'm gonna try to up my vit D intake and see if that helps. I've taken probiotics for many weeks and haven't seen improvement, so I've stopped them until I try another approach to dealing with my symptoms. I think you're right about not taking antibiotics except in the cases you mention.

Try all the metabolic avenues, but at the same time find a neuromuscular therapist in your area who has been trained to do organ massage, aka visceral manipulation. The physical component of dysbiosis is EQUAL to the functional side. Dysbiosis is facilitated by physical "kinks" and stagnations throughout the digestive system. Then, if you find the right metabolic fix, , a complete recovery can be thwarted by pockets resistant to treatment. You can even work the intestines yourself. Google search brought up a lot of junkie stuff, so that's no help. Just go sqaure inch by square inch with two or three flattened fingers on each hand in a counter clockwide motion. You will feel many many area of hardness and discomfort. Work at a level of MILD discomfort. the Pain will go away. Not only are you "dekinking" the system, the visceral manipulation is mixing good bacteria from unobstructed areas with bad bacteria from obstructed areas. Intead of introducing exogenous probiotics, which many people here and elsewhere doubt works or can ever work. Can probiotics survive the stomach acid? In this case you're using the good bacteria that's already in the gut. Endogenous good bacteria. As long as you have some good stuff, squish it around and have them fight the bad guys. A bacterial Civil War. It works for me every time. It may take more than one "battle" , but the war can be won.

Did about half hour of leg work for you and came up with Glenn Rexroad, Akron 330-929-2819. Seems real solid in ability (Over the phone?) $75 for 75 minutes. That's a good price! It will blow your mind how quickly you will feel results. I had a bout of dysbiosis that just ended after two sessions. good luck

Antibiotics is one of the main cause of dysbiosis so it's like adding fuel to the fire, imo. Often times, it encourages other diseases to enter your body. Ever notice why the use of antibiotics are restrained even more today? People are learning that you don't mess with antibiotics cause it may heal an isolated problem in your body but can put your overall health at risk. Diet is the biggest role to cure you of dysbiosis. Eat foods that are HIGH IN FIBER. Try any or all of these effective natural stuff as well: astragalus, olive leaf extract, medicinal mushroom extract, and oil of oregano. Btw, do you know what kind of dysbiosis you have? The type of diet advisable for you depends on the category of your dysbiosis.

i see..well i guess you should just look at the symptoms here and then determine what diet you should take.
Putrefaction dysbiosis occurs when we don't digest our food well, resulting in them rotting inside us. It is the most common type and may bring on bloating, discomfort, or indigestion. A diet high in animal fat and low in fiber is why this type of dysbiosis is so prevalent in many “industrialized” societies. So you may want to skip food that is very high in fat.

Deficiency dysbiosis..this type of dysbiosis is a deficiency in good bacteria such as lactobacilli. Generally, the use of antibiotics and a low fiber intake is responsible for this. Deficiency dysbiosis is often seen in those with irritable bowel syndrome and food sensitivities. As this type of dysbiosis is often seen together with putrefaction dysbiosis, take the same steps.

I agree that antibiotics often create more damage than they heal. I think doctors might be afraid that the more antibiotics they prescribe, especially when they're unnecessary, the more they're increasing resistant strains of bacteria. I'll try to increase the fiber in my diet, especially prebiotics as others have mentioned. I haven't been tested so I don't know the exact details of which bacteria are too high or low in my gut, it would def help me have a clearer picture of what's going on though.

I would say that putrefaction dysbiosis is secondary to fermentation dysbiosis. In other words, you only start to have problems with digesting proteins and fat when you develop dysbiosis and leaky gut from a diet too high in things that damage the gut and cause the bad bacteria to grow such as sugar and grains. Really you could combine all these and say there is only one "kind" of dysbiosis cause if you have a deficiency of good bacteria you'll simultaneously have fermentation and possibly putrefaction.

Fermantation dysbiosis..foods are “fermented”within our bodies, resulting in bloating, constipation, diarrhea, fatigue, and gas. This generally occurs due to the maldigestion of carbohydrates such as sugars, fruit, beer, wine, grains, and fiber. To help eliminate fermentation dysbiosis, you must avoid carbohydrate-containing foods. A diet free of cereal grains and added sugars is helpful, and some people may have to avoid fruit, fat, and added sugars is helpful, and some people may have to avoid fruit, fat, and starchy vegetables.

Sensitization dysbiosis occurs when microbes in the gut produce toxins that the body recognizes as foreign. The body then activates an immune response to kill them. However, this response may result in autoimmune diseases such as rheumatoid arthritis, ankylosing spondylitis (impaired mobility of the spinal column), and eczema. Those with sensitization dysbiosis may experience food intolerances and leaky gut syndrome. As in fermentation dysbiosis, restrict carbohydrate consumption and use friendly bacteria. So there, hope I helped somehow and good luck. :)

However, I think differences in levels of each bacteria will occur based on the individual, so maybe in that sense you could have different "kinds" of dysbiosis since there are so many different strains of bacteria that could overgrow relative to the others. I think the sum of evidence shows that it's excess carbs, especially bad carbs, that cause overgrowth of bad bacteria, not protein and fat. It's not the animal protein and fat in industrialized societies that is causing dysbiosis and gut damage, it's the trans and omega 6 fats and large amounts of sugar.

I'm sure it's dysbiosis, I've researched it for years and fit all the symptoms to a T, but I def think other things are involved, adrenal fatigue being one. Thanks for the link though I'll take the quiz, I suspect I have many of the symptoms on it.

Antibiotics are medicine that kills bacteria or slows the growth of bacteria. They are used to cure diseases. Antibiotics do not harm people. Penicillin is a popular antibiotic. Antibiotics started to be produced in 1939. Antibiotics cannot stop a virus. Antibiotics are not the same thing as antibodies.

don't do a low residue diet. i tried it. it's ridiculous and gives you a false positive. of course most of your flatulence and bloating will decrease because you don't have anything to feed it. but that does nothing for the underlying problem such as a damaged gut that got you to where you are to start, or a lack of good bacteria. soluble fiber is good for you but i agree it can be problematic by feeding the bad bacteria. this is easily fixed by ingesting probiotics alongside your soluble fiber. a much better approach! this is from experience. try acacia fiber. i find it very agreeable!

The major turning point for me was a grain, dairy, nut, nightshade, coffee, and yeast FREE diet (Paleo Autoimmune Diet).

Taking hydrochloric acid (Betaine HCI) every time I ate.

I originally thought probiotics were a scam, and many are for that matter, but some are also lifesavers. There are HUGE quality differences in probiotics, Jarro's brand was the only brand that worked for me after trying many, many different probiotic supplements.

Not related to dysbiosis in particular (but includes it) is eating the wrong foods for your blood type. All you need to do is know your blood type, go to this website http://www.dadamo.com/typebase4/typeindexer.htm and for a large list of foods, each food for each type is categorised at beneficial for your health, neutral (safe to eat) or a food to avoid. I've been on it mostly by avoiding red meat and pork (I'm type A and live at home) and have noticed a large improvement in my bowel movements, little indigestion, much more energy and feeling healthier overall.

The best thing you can do is to avoid eating lots of fermentable fiber(Soluble fiber, prebiotics) that feed bacteria. You gotta starve it out, they need to die off. I agree with Dean. Go on a low carb/fiber diet and eat a more a higher fat/animal protein diet. Avoid all fruits, high fructose vegetables, simple refined sugars and sweeteners, starches, lactose and most FODMAPS. Eat mostly fish, seafood, eggs, beef, lamb, chicken, turkey, buffalo. Raw virgin coconut oil helps balance intestinal flora. Use olive oils, ghee, grassfed butter (kerrygold), avocado oils and eat some nuts and seeds occasionally. If all else fails, get medical help. I hope your condition improves and you feel better. It sucks going through life feeling crap all the time:(. You know what else might help? high quality Colostrum.

Dean,
I disagree. Peat recommends carrots because they are so anti-bacterial and anti-fungal that they resist digestion from the bad bacteria, and are supposed to help kill them off. Also the carrots stimulate peristalsis which can help move bad bacteria down the line, and out of the body. Peat also suggest cooked bamboo shoots for the same effect. Other raw vegetables are the ones that are problematic, that is why Peat specifically recommends carrots.

I haven't really tried the daily carrot salad full on as I don't have severe digestive issues but I've heard anecdotes that it can do wonders. This is in the context of a low fiber high sugar diet though. Carrots are cheap though and readily available so its worth a shot imo.

"How did it make it worse?" - worsening of symptoms I had whenever I ate carbs/vegetables/FODMAPs
"What did the rest of your diet look like? Did you eat the carrot salad solo?" - I was VLC, raw carrots clearly stood out from the rest of my diet.
"Have you cured your digestive issue?" - short answer is yes. VLC works, but it takes time.

You need to understand that Ray Peat recommends carrots to "soak up" toxins in the colon, but that's a problematic assumption. Reaching the colon partly undigested means the chyme can ferment. Raw vegetables are very hard to digest and should be avoided when someone has SIBO. Carrots are loaded with fructose and even gram amounts can be problematic in these cases.